public void UpdateModifiers(IReactionBuilder reaction, string moleculeName, string compoundName, Simulation simulation)
{
AllInteractionProcessesFor(moleculeName, compoundName, simulation).Each((process, i) =>
{
var inhibitor = process.ParentCompound;
if (!reaction.ModifierNames.Contains(inhibitor.Name))
{
reaction.AddModifier(inhibitor.Name);
}
});
}
protected override void ExecuteWith(IMoBiContext context)
{
base.ExecuteWith(context);
_reaction.RemoveModifier(_oldModifier);
_reaction.AddModifier(_newModifier);
var reactionDiagramManager = _buildingBlock.DiagramManager.DowncastTo <IMoBiReactionDiagramManager>();
if (reactionDiagramManager.IsInitialized)
{
reactionDiagramManager.RenameMolecule(_reaction, _oldModifier, _newModifier);
}
context.PublishEvent(new RemovedReactionModifierEvent(_reaction, _oldModifier));
context.PublishEvent(new AddedReactionModifierEvent(_reaction, _newModifier));
}
protected override void Context()
{
base.Context();
var formula = new ExplicitFormula().WithFormulaString("123").WithName("TOTO");
formula.AddObjectPath(new FormulaUsablePath(new[] { "Organism", CoreConstants.KeyWords.Molecule }));
formula.AddObjectPath(new FormulaUsablePath(new[] { "Organism", CoreConstants.Molecule.DrugFcRnComplexTemplate }));
_reaction = new PKSimReaction().WithName("xx").WithId("xx").WithFormula(formula);
_reaction.AddEduct(new ReactionPartnerBuilder(CoreConstants.KeyWords.Molecule, 1));
_reaction.AddEduct(new ReactionPartnerBuilder("XY", 1));
_reaction.AddProduct(new ReactionPartnerBuilder(CoreConstants.Molecule.DrugFcRnComplexTemplate, 1));
_reaction.AddModifier(CoreConstants.KeyWords.Molecule);
_formulaCache = new BuildingBlockFormulaCache();
A.CallTo(() => _cloneManager.Clone(_reaction)).Returns(_reaction);
}
/// <summary>
/// Imports the SBML Modifiers to MoBi Modifiers.
/// </summary>
private void CreateModifiers(Reaction sbmlReaction, IReactionBuilder reactionBuilder, string reactionCompartment, Model model)
{
for (long i = 0; i < sbmlReaction.getNumModifiers(); i++)
{
var modifier = sbmlReaction.getModifier(i);
if (ModifierInDifferentCompartment(reactionCompartment, modifier, model))
{
continue;
}
var modifierMolecule = _sbmlInformation.GetMoleculeBySBMLId(modifier.getSpecies());
if (modifierMolecule != null)
{
reactionBuilder.AddModifier(modifierMolecule.Name);
}
}
}
private void replaceKeywordsInProcess(IReactionBuilder reactionBuilder, string[] keywords, string[] replacementValues)
{
replaceFormulaKeywords(reactionBuilder, keywords, replacementValues);
reactionBuilder.Parameters.Each(p => replaceFormulaKeywords(p, keywords, replacementValues));
foreach (var reactionPartner in reactionBuilder.Educts.Union(reactionBuilder.Products))
{
reactionPartner.MoleculeName = reactionPartner.MoleculeName.ReplaceKeywords(keywords, replacementValues);
}
var replacedModifiers = new List <string>();
foreach (var modifier in reactionBuilder.ModifierNames)
{
replacedModifiers.Add(modifier.ReplaceKeywords(keywords, replacementValues));
}
reactionBuilder.ClearModifiers();
foreach (var replacedModifier in replacedModifiers)
{
reactionBuilder.AddModifier(replacedModifier);
}
}
protected override void Context()
{
base.Context();
_reaction = new ReactionBuilder();
_reaction.AddModifier(_compound1.Name);
}